Observing Short-Term Geomorphic Change in a Human-Modified River Using Terrestrial Repeat Photographs and Traditional Surveys: Uncompahgre River, Colorado, USA

The Uncompahgre River in Ouray, CO, was modified in 1996 from a braided river system to a meandering river channel. Large boulders of riprap were placed along designed meanders to prevent erosion and enable the development of permanent human structures on the flood plain. Deposition of gravel bars in the modified channel occurs annually during the summer. This gravel is "mined" by the City of Ouray; however, the effects of this excavation and the original modification were never assessed. This study provides an assessment by quantifying cross-sectional area change, cumulative grain-size distributions, shear stresses, slopes, and sinuosities using traditional survey methods. In addition, volume change of a gravel bar inside the modified channel was estimated using extreme oblique photographs (>45 degrees from nadir) that were obtained from nearby cliffs. Close-range photogrammetry was used in the natural channel downstream to evaluate photogrammetric methods using different lenses, image sensors, and camera geometries. Both traditional and photogrammetric methods clearly indicated significant deposition in the modified channel, whereas erosion occurred directly downstream from the modified channel, but did not occur at a reach 1.5 km downstream. In the natural channel, no cross-sectional area change occurred, grains were poorly sorted, and the longitudinal slope was ~four times steeper than the modified channel. Shear stress ratios were used as an erosion threshold, which did not correlate with actual cross-sectional area change, but a decrease in shear stress ratios from May 2011 to September 2011 were associated with erosion. Average RMSE values for DEMs created from extremeoblique photographs of a gravel bar in May 2011 and September 2011 were 0.140 m and 0.324 m, respectively. Using a DEM of difference with a t-statistic filter revealed that 115m3 of gravel was deposited. The Uncompahgre River showed similar geomorphic characteristics to other rivers in southwest Colorado, however, the slope of the natural and modified channels were much steeper than other rivers. Extreme-oblique photography and unconventional sensors both yielded reliable results, showing that these atypical techniques can be used in terrestrial photogrammetric applications such as, post-restoration assessments, as long as proper base-to-height ratios are achieved

Advanced methods for relightable scene representations in image space

The realistic reproduction of visual appearance of real-world objects requires accurate computer graphics models that describe the optical interaction of a scene with its surroundings. Data-driven approaches that model the scene globally as a reflectance field function in eight parameters deliver high quality and work for most material combinations, but are costly to acquire and store. Image-space relighting, which constrains the application to create photos with a virtual, fix camera in freely chosen illumination, requires only a 4D data structure to provide full fidelity. This thesis contributes to image-space relighting on four accounts: (1) We investigate the acquisition of 4D reflectance fields in the context of sampling and propose a practical setup for pre-filtering of reflectance data during recording, and apply it in an adaptive sampling scheme. (2) We introduce a feature-driven image synthesis algorithm for the interpolation of coarsely sampled reflectance data in software to achieve highly realistic images. (3) We propose an implicit reflectance data representation, which uses a Bayesian approach to relight complex scenes from the example of much simpler reference objects. (4) Finally, we construct novel, passive devices out of optical components that render reflectance field data in real-time, shaping the incident illumination into the desired imageDie realistische Wiedergabe der visuellen Erscheinung einer realen Szene setzt genaue Modelle aus der Computergraphik für die Interaktion der Szene mit ihrer Umgebung voraus. Globale Ansätze, die das Verhalten der Szene insgesamt als Reflektanzfeldfunktion in acht Parametern modellieren, liefern hohe Qualität für viele Materialtypen, sind aber teuer aufzuzeichnen und zu speichern. Verfahren zur Neubeleuchtung im Bildraum schränken die Anwendbarkeit auf fest gewählte Kameras ein, ermöglichen aber die freie Wahl der Beleuchtung, und erfordern dadurch lediglich eine 4D - Datenstruktur für volle Wiedergabetreue. Diese Arbeit enthält vier Beiträge zu diesem Thema: (1) wir untersuchen die Aufzeichnung von 4D Reflektanzfeldern im Kontext der Abtasttheorie und schlagen einen praktischen Aufbau vor, der Reflektanzdaten bereits während der Messung vorfiltert. Wir verwenden ihn in einem adaptiven Abtastschema. (2) Wir führen einen merkmalgesteuerten Bildsynthesealgorithmus für die Interpolation von grob abgetasteten Reflektanzdaten ein. (3) Wir schlagen eine implizite Beschreibung von Reflektanzdaten vor, die mit einem Bayesschen Ansatz komplexe Szenen anhand des Beispiels eines viel einfacheren Referenzobjektes neu beleuchtet. (4) Unter der Verwendung optischer Komponenten schaffen wir passive Aufbauten zur Darstellung von Reflektanzfeldern in Echtzeit, indem wir einfallende Beleuchtung direkt in das gewünschte Bild umwandeln

Real-time tissue viability assessment using near-infrared light

Despite significant advances in medical imaging technologies, there currently exist no tools to effectively assist healthcare professionals during surgical procedures. In turn, procedures remain subjective and dependent on experience, resulting in avoidable failure and significant quality of care disparities across hospitals. Optical techniques are gaining popularity in clinical research because they are low cost, non-invasive, portable, and can retrieve both fluorescence and endogenous contrast information, providing physiological information relative to perfusion, oxygenation, metabolism, hydration, and sub-cellular content. Near-infrared (NIR) light is especially well suited for biological tissue and does not cause tissue damage from ionizing radiation or heat. My dissertation has been focused on developing rapid imaging techniques for mapping endogenous tissue constituents to aid surgical guidance. These techniques allow, for the first time, video-rate quantitative acquisition over a large field of view (> 100 cm2) in widefield and endoscopic implementations. The optical system analysis has been focused on the spatial-frequency domain for its ease of quantitative measurements over large fields of view and for its recent development in real-time acquisition, single snapshot of optical properties (SSOP) imaging. Using these methods, this dissertation provides novel improvements and implementations to SSOP, including both widefield and endoscopic instrumentations capable of video-rate acquisition of optical properties and sample surface profile maps. In turn, these measures generate profile-corrected maps of hemoglobin concentration that are highly beneficial for perfusion and overall tissue viability. Also utilizing optical property maps, a novel technique for quantitative fluorescence imaging was also demonstrated, showing large improvement over standard and ratiometric methods. To enable real-time feedback, rapid processing algorithms were designed using lookup tables that provide a 100x improvement in processing speed. Finally, these techniques were demonstrated in vivo to investigate their ability for early detection of tissue failure due to ischemia. Both pre-clinical studies show endogenous contrast imaging can provide early measures of future tissue viability. The goal of this work has been to provide the foundation for real-time imaging systems that provide tissue constituent quantification for tissue viability assessments.2018-01-09T00:00:00

NASA Tech Briefs, Februrary 2013

Topics covered include: Measurements of Ultra-Stable Oscillator (USO) Allan Deviations in Space; Gaseous Nitrogen Orifice Mass Flow Calculator; Validation of Proposed Metrics for Two-Body Abrasion Scratch Test Analysis Standards; Rover Low Gain Antenna Qualification for Deep Space Thermal Environments; Automated, Ultra-Sterile Solid Sample Handling and Analysis on a Chip; Measuring and Estimating Normalized Contrast in Infrared Flash Thermography; Spectrally and Radiometrically Stable, Wideband, Onboard Calibration Source; High-Reliability Waveguide Vacuum/Pressure Window; Methods of Fabricating Scintillators With Radioisotopes for Beta Battery Applications; Magnetic Shield for Adiabatic Demagnetization Refrigerators (ADR); CMOS-Compatible SOI MESFETS for Radiation-Hardened DC-to-DC Converters; Silicon Heat Pipe Array; Adaptive Phase Delay Generator; High-Temperature, Lightweight, Self-Healing Ceramic Composites for Aircraft Engine Applications; Treatment to Control Adhesion of Silicone-Based Elastomers; High-Temperature Adhesives for Thermally Stable Aero-Assist Technologies; Rockballer Sample Acquisition Tool; Rock Gripper for Sampling, Mobility, Anchoring, and Manipulation; Advanced Magnetic Materials Methods and Numerical Models for Fluidization in Microgravity and Hypogravity; Data Transfer for Multiple Sensor Networks Over a Broad Temperature Range; Using Combustion Synthesis to Reinforce Berms and Other Regolith Structures; Visible-Infrared Hyperspectral Image Projector; Three-Axis Attitude Estimation With a High-Bandwidth Angular Rate Sensor Change_Detection.m; AGATE: Adversarial Game Analysis for Tactical Evaluation; Ionospheric Simulation System for Satellite Observations and Global Assimilative; Modeling Experiments (ISOGAME); An Extensible, User- Modifiable Framework for Planning Activities; Mission Operations Center (MOC) - Precipitation Processing System (PPS) Interface Software System (MPISS); Automated 3D Damaged Cavity Model Builder for Lower Surface Acreage Tile on Orbiter; Mixed Linear/Square-Root Encoded Single-Slope Ramp Provides Low-Noise ADC with High Linearity for Focal Plane Arrays; RUSHMAPS: Real-Time Uploadable Spherical Harmonic Moment Analysis for Particle Spectrometers; Powered Descent Guidance with General Thrust-Pointing Constraints; X-Ray Detection and Processing Models for Spacecraft Navigation and Timing; and Extreme Ionizing-Radiation-Resistant Bacteriu

From cellular vulnerability to altered circuit activity:a systems biology approach to study amyotrophic lateral sclerosis

The devastating effects of the brain losing its ability to control voluntary body movement are illustrated by diseases such as amyotrophic lateral sclerosis (ALS) - where the nerve cells that allow the brain to effectively communicate with muscles are progressively lost. Most of the ALS research traditionally revolves around the affected nerve cells, known as motoneurons, and aims to rescue their decline in function. Motoneurons are however part of larger networks in the nervous system and constantly receive, process and transmit signals. Therefore, even the smallest alteration of a single motoneuron will likely leave a mark on its connecting neurons and vice versa. Could it be that solely targeting the function of diseased neurons has unexpected effects in an already (mal)adapted network? To mimic ALS, we used the worm Caenorhabditis elegans engineered to express the human gene TDP-43. Dysregulated TDP-43 is considered a uniform hallmark of ALS and its expression in C. elegans causes severe paralysis. By developing and combining numerous technology-driven, mostly unbiased screening approaches we show that TDP-43 impedes neuronal function and causes an imbalance between stimulatory and inhibitory signals in the motor circuit. While functional output of repressed motoneurons could be restored via modulation of their activity, these interventions did not result in improved locomotion. Rebalancing the derailed motor circuit dynamics by combining multiple treatments, however, effectively restored movement. Because of the high degree of similarity in genetic alterations and pathology between ALS worms and patients, similar therapeutic strategies may eventually be valuable for ALS patients

Assessing motor-related phenotypes of Caenorhabditis elegans with the wide field-of-view nematode tracking platform

Caenorhabditis elegans is a valuable model organism in biomedical research that has led to major discoveries in the fields of neurodegeneration, cancer and aging. Because movement phenotypes are commonly used and represent strong indicators of C. elegans fitness, there is an increasing need to replace manual assessments of worm motility with automated measurements to increase throughput and minimize observer biases. Here, we provide a protocol for the implementation of the improved wide field-of-view nematode tracking platform (WF-NTP), which enables the simultaneous analysis of hundreds of worms with respect to multiple behavioral parameters. The protocol takes only a few hours to complete, excluding the time spent culturing C. elegans, and includes (i) experimental design and preparation of samples, (ii) data recording, (iii) software management with appropriate parameter choices and (iv) post-experimental data analysis. We compare the WF-NTP with other existing worm trackers, including those having high spatial resolution. The main benefits of WF-NTP relate to the high number of worms that can be assessed at the same time on a whole-plate basis and the number of phenotypes that can be screened for simultaneously

Observing Short-Term Geomorphic Change in a Human-Modified River Using Terrestrial Repeat Photographs and Traditional Surveys: Uncompahgre River, Colorado, USA

The Uncompahgre River in Ouray, CO, was modified in 1996 from a braided river system to a meandering river channel. Large boulders of riprap were placed along designed meanders to prevent erosion and enable the development of permanent human structures on the flood plain. Deposition of gravel bars in the modified channel occurs annually during the summer. This gravel is "mined" by the City of Ouray; however, the effects of this excavation and the original modification were never assessed. This study provides an assessment by quantifying cross-sectional area change, cumulative grain-size distributions, shear stresses, slopes, and sinuosities using traditional survey methods. In addition, volume change of a gravel bar inside the modified channel was estimated using extreme oblique photographs (>45 degrees from nadir) that were obtained from nearby cliffs. Close-range photogrammetry was used in the natural channel downstream to evaluate photogrammetric methods using different lenses, image sensors, and camera geometries. Both traditional and photogrammetric methods clearly indicated significant deposition in the modified channel, whereas erosion occurred directly downstream from the modified channel, but did not occur at a reach 1.5 km downstream. In the natural channel, no cross-sectional area change occurred, grains were poorly sorted, and the longitudinal slope was ~four times steeper than the modified channel. Shear stress ratios were used as an erosion threshold, which did not correlate with actual cross-sectional area change, but a decrease in shear stress ratios from May 2011 to September 2011 were associated with erosion. Average RMSE values for DEMs created from extremeoblique photographs of a gravel bar in May 2011 and September 2011 were 0.140 m and 0.324 m, respectively. Using a DEM of difference with a t-statistic filter revealed that 115m3 of gravel was deposited. The Uncompahgre River showed similar geomorphic characteristics to other rivers in southwest Colorado, however, the slope of the natural and modified channels were much steeper than other rivers. Extreme-oblique photography and unconventional sensors both yielded reliable results, showing that these atypical techniques can be used in terrestrial photogrammetric applications such as, post-restoration assessments, as long as proper base-to-height ratios are achieved

Quantitative phase imaging: advances to 3D imaging and applications to neuroscience

This thesis provides a brief overview of quantitative phase imaging (QPI) methods along with applications and advances made on them. First, spatial light interference microscopy (SLIM) is introduced as a QPI method extensively used in this thesis. Using this setup, an application of QPI in neuroscience is demonstrated by studying the emergent formation of a neuronal network. Second, an expansion of this QPI method into a 3D quantitative imaging method, called white-light diffraction tomography (WDT), has been shown. Lastly, an initial result for another advance in SLIM is introduced by combining SLIM with a programmable illumination. In the first part of this work, the emergent self-organization of a neuronal network has been demonstrated using the SLIM system. The emergent self-organization of a neuronal network in a developing nervous system is the result of a remarkably orchestrated process involving a multitude of chemical, mechanical and electrical signals. Little is known about the dynamic behavior of a developing network (especially in a human model) primarily due to a lack of practical and non-invasive methods to measure and quantify the process. Using the SLIM system, several fundamental properties of neuronal networks have been measured non-invasively from the sub-cellular to the cell population level. This method quantifies network formation in human stem cell derived neurons and shows correlations between trends in the growth, transport, and spatial organization of such a system, by utilizing the quantitative phase data with novel analysis tools, including dispersion-relation phase spectroscopy (DPS). A deeper understanding of neuronal network formation has been provided by studying filopodia dynamics in neurons. By measuring the dry mass change over time and several other new metrics, it is shown that the filopodia dynamics successfully reflect the expected neurite outgrowth. In the second part, white-light diffraction tomography (WDT) is introduced as a new approach for imaging microscopic transparent objects such as live unlabeled cells in 3D. The approach extends diffraction tomography to white light illumination and imaging rather than scattering plane measurements. The experiments were performed using the SLIM system. The axial dimension of the object was reconstructed by scanning the focus through the object and acquiring a stack of phase-resolved images. The 3D structures of live, unlabeled red blood cells are imaged and compared with confocal and scanning electron microscopy images. The 350 nm transverse and 900 nm axial resolution achieved allows us to reveal sub-cellular structures at high resolution in E. coli cells and HT29 cells. Furthermore, a 4D imaging capability, with the fourth dimension being time, has also been demonstrated. The WDT theory is further extended to explain light scattering through thick tissue, which is not in the single scattering regime. The obtained inverse scattering solution for thick samples is then related to the time-reversal theory, and it is proven that there are strong constraints for time-reversal to work. By introducing a few specific examples, including scattering through a particle and scattering through a grating, the physics of light scattering and time-reversal theory is deeply understood. Lastly, an upgrade to the SLIM system with a programmable illumination source, a projector, has been demonstrated. By replacing the ring illumination of PC with a ring-shaped pattern projected onto the condenser plane, results comparable to those of the original SLIM were recovered. This new method minimized the halo artifact of the imaging system by minimizing the effect of spatial coherence caused by the thickness of the illumination. Further application of this technique into optogenetics is introduced and the initial results are presented

Modeling and Simulation in Engineering

This book provides an open platform to establish and share knowledge developed by scholars, scientists, and engineers from all over the world, about various applications of the modeling and simulation in the design process of products, in various engineering fields. The book consists of 12 chapters arranged in two sections (3D Modeling and Virtual Prototyping), reflecting the multidimensionality of applications related to modeling and simulation. Some of the most recent modeling and simulation techniques, as well as some of the most accurate and sophisticated software in treating complex systems, are applied. All the original contributions in this book are jointed by the basic principle of a successful modeling and simulation process: as complex as necessary, and as simple as possible. The idea is to manipulate the simplifying assumptions in a way that reduces the complexity of the model (in order to make a real-time simulation), but without altering the precision of the results